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- PDB-1t05: HIV-1 reverse transcriptase crosslinked to template-primer with t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1t05 | ||||||
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Title | HIV-1 reverse transcriptase crosslinked to template-primer with tenofovir-diphosphate bound as the incoming nucleotide substrate | ||||||
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![]() | Transferase/DNA / HIV-1 reverse transcriptase / tenofovir / RT-DNA complex / Transferase-DNA COMPLEX | ||||||
Function / homology | ![]() integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / Assembly Of The HIV Virion / retroviral ribonuclease H / exoribonuclease H / Budding and maturation of HIV virion / exoribonuclease H activity / protein processing / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / peptidase activity / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tuske, S. / Sarafianos, S.G. / Ding, J. / Arnold, E. | ||||||
![]() | ![]() Title: Structures of HIV-1 RT-DNA complexes before and after incorporation of the anti-AIDS drug tenofovir Authors: Tuske, S. / Sarafianos, S.G. / Clark Jr., A.D. / Ding, J. / Naeger, L.K. / White, K.L. / Miller, M.D. / Gibbs, C.S. / Boyer, P.L. / Clark, P. / Wang, G. / Gaffney, B.L. / Jones, R.A. / ...Authors: Tuske, S. / Sarafianos, S.G. / Clark Jr., A.D. / Ding, J. / Naeger, L.K. / White, K.L. / Miller, M.D. / Gibbs, C.S. / Boyer, P.L. / Clark, P. / Wang, G. / Gaffney, B.L. / Jones, R.A. / Jerina, D.M. / Hughes, S.H. / Arnold, E. | ||||||
History |
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Remark 999 | SEQUENCE RESIDUE MRG 817 OF THE P CHAIN IS CROSSLINKED TO CHAIN A RESIDUE C258. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 236.9 KB | Display | ![]() |
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PDB format | ![]() | 183.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1t03C ![]() 1rtdS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Oligonucleotide ... , 2 types, 2 molecules TP
#1: DNA chain | Mass: 8383.385 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 6474.268 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: chemically modified with thiol-dGMP and enzymatically terminated with ddGTP |
-Protein , 2 types, 2 molecules AB
#3: Protein | Mass: 64249.660 Da / Num. of mol.: 1 / Fragment: HIV-1 reverse transcriptase p66 subunit / Mutation: Q258C, C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#4: Protein | Mass: 51123.629 Da / Num. of mol.: 1 / Fragment: HIV-1 reverse transcriptase p51 subunit / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 4 types, 29 molecules ![](data/chem/img/MG.gif)
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#5: Chemical | #6: Chemical | ChemComp-TNV / [ | #7: Chemical | ChemComp-GOL / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.9 Å3/Da / Density % sol: 75 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 50 mM MES, pH 6.4, 100 mM ammonium sulfate, 5% sucrose, 5% glycerol, 10% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 108 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 12, 2002 / Details: wiggler |
Radiation | Monochromator: wiggler / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 3→40 Å / Num. obs: 52624 / % possible obs: 91.3 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 46 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 3→3.11 Å / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 1.2 / Num. unique all: 2649 / % possible all: 50.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1RTD Resolution: 3→20 Å / σ(F): 1.1 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.05 Å /
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